1.1 Submission Form

1.2 MERFISH Data Quality

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Generally, log10 transcript count > 4.0 for human brain sample in most FOC can be considered as a good quality standard.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

1.3 MERFISH Sample Index

1.3.1 H250, (Control_1)

1.3.2 MN28, (ALS_1)

1.3.3 H260, (Control_2)

1.3.4 MN13, (ALS_2)

1.3.5 H264, (Control_3)

1.3.6 MN32, (ALS_3)

1.3.7 H262, (Control_4)

1.3.8 MN40, (ALS_4)

1.3.9 , H246 ( Failure Sample!)

1.3.10 , MN31 ( Failure Sample!)

2.1 Cell Segmentation

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 2500].

2.2 Transcript level

2.3 Cell Annotation

We performed cell annotation by applying Leiden clustering to all cells across all samples. This clustering method subgrouped the cells based on their gene expression profiles. Then, for each identified cluster, we defined their cell types by matching the differential expression gene with known cell type markers.

2.3.1 Cell Type Umap

2.3.2 Cell Count Table

2.3.3 Cell Type Spatial Map

3.1 ANXA11

3.2 ATXN1

3.3 ATXN2

3.4 C9orf72

3.5 CAMTA1

3.6 CFAP410

3.7 CHCHD10

3.8 ENAH

3.9 EPHA4

3.10 FUS

3.11 HFE

3.12 HNRNPA1

3.13 KIF5A

3.14 NEK1

3.15 NIPA1

3.16 OPTN

3.17 PFN1

3.18 SCFD1

3.19 SOD1

3.20 TARDBP

3.21 TBK1

3.22 TUBA4A

3.23 UBQLN2

3.24 UNC13A

3.25 VAPB

3.26 VCP

4.1 Glutamatergic

4.1.1 Glutamatergic DE Volcano

4.1.2 Glutamatergic DE Table

4.2 GABAergic

4.2.1 GABAergic DE Volcano

4.2.2 GABAergic DE Table